Continue WEMD Simulation Guided by CryoEM Maps

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Role-based/Structural Biologist

  • Solution-based/Target Identification/Target Preparation

  • Task-based/Target Prep & Analysis/Protein Preparation

  • Product-based/Molecular Dynamics/WESTPA

Description

This floe continues a previous WEMD simulation for sampling the diverse conformational states of a protein guided by different types of cryo-EM maps. Generally, this floe is used to perform long WEMD simulations using more advanced options or to continue a simulation that was stopped unexpectedly. Namely, this floe can be used to continue simulations from these automated floes: Automated WEMD Simulation and Best Structure Search Guided by Target Cryo-EM Map and Automated WEMD Simulation and Best Structure Search Guided By Eigen Cryo-EM Maps. However, the best structure match needs to be done in a separate floe. Caution: This floe can be expensive for large systems using 2D eigenmaps, even when the default settings are used (more than $1000 for systems with greater than 1000 residues).

Promoted Parameters

Title in user interface (promoted name)

Weighted Ensemble Parameters

Total Cumulative Number of Iterations (iterations): Desired number of iterations, including all previous simulations.

  • Required

  • Type: integer

Inputs

Collection (collection): Protein sampling data generated in the previous round of weighted ensemble MD simulation. Simulation data generated in this run will be added to this input collection.

  • Required

  • Type: collection_source

  • Default: wemd_simulation_collection

Outputs

Failure Report (fail_report): Output report to generate upon failure.

  • Type: string

  • Default: Protein Sampling Failure Report

Output Dataset (simulation_data_out): Output dataset to which to write.

  • Required

  • Type: dataset_out

  • Default: WESimulation_Dataset_Out

Reweighting Option

Reweighting (reweighting): Toggle on to periodically reweight trajectory walkers using WESS or WEED plugin (for non-equilibrium steady state or equilibrium sampling, respectively).

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Number of Bins for Reweighting (reweighting_nbins): Number of bins for automatic reweighting. (use the JSON File Reweighting input to set reweighting bins manually)

  • Type: integer

  • Default: 10

Reweighting Period (reweighting_period): The period of reweighting the trajectory segments in terms of the number of iterations. No reweighting when set to 0. This parameter will be set to the value specified here when resuming a simulation.

  • Required

  • Type: integer

  • Default: 50

Reweighting Window Size (reweighting_window): The fraction of previous iterations used for estimating the transition rates for reweighting. This parameter will be set to the value specified here when resuming a simulation.

  • Required

  • Type: decimal

  • Default: 0.75

Report Settings

Floe Report (simulation_report_out): The title for the output floe report.

  • Required

  • Type: string

  • Default: Continue WEMD Simulation Report

Number of iterations for averaged distributions (average_window): Number of iterations to generate averaged density distributions for calculating the Kullback-Leibler divergence in each dimension.

  • Type: integer

  • Default: 2

Number of Bins for Histogram (n_bins): Number of bins for plotting the density distribution in each dimension.

  • Type: integer

  • Default: 50

Option for reference PDF (ref_type): Set type of reference probability distribution function for KL divergence.

  • Type: string

  • Default: Accumulated

  • Choices: [‘Accumulated’, ‘Averaged’]

Orion settings for cost optimization of WEMD simulation

Spot policy (spot_policy): Control cube placement on spot market instances

  • Type: string

  • Default: Required

  • Choices: [‘Allowed’, ‘Preferred’, ‘NotPreferred’, ‘Prohibited’, ‘Required’]

Instance Type (instance_type): The type of instance that this cube needs to be run on

  • Type: string

Maximum number of Parallel Cubes for MD (max_parallel): The maximum number of concurrently running copies of this Cube

  • Type: integer

  • Default: 1000